NeuroQP Docs

Uploading your data

In the Data view, you can drag and drop files or click Browse files to select images.

File upload happens in two stages: staging and upload.

1. File selection and organization

Selected files show detected animal names, stainings, magnification, slice coordinate, brain region, and hemisphere when required.

At this stage, nothing has been uploaded yet. Review the detected values and fix any issues before starting the upload.

2. Uploading

Once the staged files look correct, click Upload.

Keep the page open until upload completes.

How metadata detection works

From each filename, NeuroQP tries to detect:

  • Animal
  • Staining, including aliases
  • Magnification (4x, 10x, or 20x)
  • Slice coordinate or atlas label, usually AP for brain projects or a spinal segment label for spinal cord projects
  • Brain region, for Detail only projects
  • Hemisphere, for Detail only projects in Separate hemisphere mode

The app matches detected values against your Study setup and the image slots required by the project's acquisition mode and image roles.

Filename best practices

Use predictable filenames that include the key metadata parts.

Recommended structure for registered projects:

  • [Animal]_[Staining]_[Magnification]_AP[-n.nn].ext

Example for a 4x reference + detail 10x project:

FilenameAnimalStainingMagnificationAP coords
M001_DAPI_4x_AP-1.25.tifM001DAPI4x-1.25
M001_DAPI_10x_AP-1.25.tifM001DAPI10x-1.25
M001_cFos_10x_AP-1.25.tifM001cFos10x-1.25

Example for a high-res whole-slice 20x independent marker detection project:

FilenameAnimalStainingMagnificationAP coords
M001_cFos_20x_AP-1.25.tifM001cFos20x-1.25
M001_TRAP_20x_AP-1.25.tifM001TRAP20x-1.25

For mouse spinal cord projects, you can use spinal segment labels such as C1, T9, or L3 in filenames. NeuroQP will detect supported atlas labels during upload staging.

Examples:

  • M001_DAPI_10x_T9.tif
  • M001_cFos_10x_T9.tif

Exact RC coordinates are still supported, but spinal cord datasets do not have a single common Bregma-style coordinate convention. When possible, use spinal segment labels because they are usually easier to review and communicate.

For Detail only projects, include the intended brain region in the filename when possible, or assign it during staging before upload.

If hemisphere mode is Separate, also include the hemisphere when possible. NeuroQP detects left, right, l, and r when they appear as separate filename tokens.

Examples:

  • M001_CA1_left_DAPI_20x_AP-1.25.tif
  • M001_CA1_right_cFos_20x_AP-1.25.tif
  • M001_CA1_l_DAPI_20x_AP-1.25.tif
  • M001_CA1_r_cFos_20x_AP-1.25.tif

Batch strategy

Instead of uploading hundreds of images at once, it is usually best to upload in multiple batches, for example one animal at a time.

Confirm warnings are resolved before starting large uploads.

Common staging warnings

  • Unknown animal: No animal was detected in the filename.
  • Staining not detected: No configured staining or alias was detected.
  • Magnification not detected: 4x, 10x, or 20x was not detected.
  • Slice coordinate missing: NeuroQP expects a value such as AP-1.25 for brain projects, or a supported coordinate or atlas label for spinal cord projects.
  • Brain region not detected: Detail only projects need each slice assigned to a brain region.
  • Assign a hemisphere: Detail only projects in Separate hemisphere mode need each slice assigned to Left or Right for hemisphere-split Statistics.
  • Hemisphere ambiguous: Both left and right were detected in the filename. Choose the correct hemisphere before uploading.
  • Missing required role image: A slice is missing an image required by the project acquisition mode and image roles.
  • Duplicate filenames: The filename appears to have been uploaded already.

Critical warnings should be resolved before upload to avoid incomplete processing later.

After upload succeeds, processing starts automatically when prerequisites are available.